FMO DATABASE

FMODB ID: 762NK

Calculation Name: 2P84-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P84

Chain ID: A

ChEMBL ID:

UniProt ID: Q4ZC86

Base Structure: X-ray

Registration Date: 2023-09-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	133
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1220198.267341
FMO2-HF: Nuclear repulsion	1164486.072824
FMO2-HF: Total energy	-55712.194517
FMO2-MP2: Total energy	-55875.013322

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-11.9	-14.66	27.666	-10.791	-14.114	-0.058

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.044 / q_NPA : -0.028

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	5	PRO	0	0.053	0.058	3.780	-3.141	0.385	0.019	-1.904	-1.641	-0.006
4	A	6	LYS	1	0.951	0.985	6.097	-0.825	-0.825	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.050	0.018	5.583	0.131	0.131	0.000	0.000	0.000	0.000
6	A	8	ARG	1	0.793	0.868	10.697	0.228	0.228	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.777	-0.867	14.317	-0.419	-0.419	0.000	0.000	0.000	0.000
8	A	10	PHE	0	0.014	-0.003	16.684	0.034	0.034	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.707	-0.857	20.406	-0.253	-0.253	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.957	0.963	22.696	0.153	0.153	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.807	-0.897	26.091	-0.128	-0.128	0.000	0.000	0.000	0.000
12	A	14	ARG	1	0.782	0.888	18.935	0.315	0.315	0.000	0.000	0.000	0.000
13	A	15	HIS	0	-0.019	-0.023	25.951	0.003	0.003	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.751	0.883	27.276	0.145	0.145	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.048	-0.012	28.744	0.013	0.013	0.000	0.000	0.000	0.000
16	A	18	ASP	-1	-0.888	-0.934	29.470	-0.102	-0.102	0.000	0.000	0.000	0.000
17	A	19	TYR	0	-0.100	-0.059	28.214	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	20	GLN	0	-0.091	-0.058	25.320	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	21	LYS	1	1.000	1.004	22.236	0.184	0.184	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.102	0.050	22.796	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.062	-0.006	18.780	-0.038	-0.038	0.000	0.000	0.000	0.000
22	A	24	SER	0	-0.016	0.010	16.572	-0.012	-0.012	0.000	0.000	0.000	0.000
23	A	25	TYR	0	0.001	-0.017	14.097	-0.026	-0.026	0.000	0.000	0.000	0.000
24	A	26	ALA	0	-0.005	-0.004	9.945	0.003	0.003	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.983	-0.968	10.231	-0.569	-0.569	0.000	0.000	0.000	0.000
26	A	28	GLN	0	-0.061	-0.050	1.628	6.117	-5.211	19.995	-4.365	-4.302	-0.007
27	A	29	GLN	0	-0.004	-0.001	6.506	0.203	0.203	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-0.823	-0.918	2.335	-9.137	-7.241	3.478	-2.215	-3.158	-0.029
29	A	31	PHE	0	-0.063	-0.043	4.347	0.597	0.668	-0.001	-0.022	-0.049	0.000
30	A	32	ASP	-1	-0.917	-0.969	5.888	-0.558	-0.558	0.000	0.000	0.000	0.000
31	A	33	MET	0	-0.102	-0.046	8.124	0.144	0.144	0.000	0.000	0.000	0.000
32	A	34	GLY	0	-0.012	0.003	4.403	0.056	0.096	-0.001	-0.010	-0.029	0.000
33	A	35	PHE	0	0.011	-0.001	2.200	-4.511	-1.552	4.176	-2.240	-4.895	-0.016
34	A	36	THR	0	-0.018	0.005	4.350	0.270	0.346	0.000	-0.035	-0.040	0.000
35	A	37	ILE	0	-0.015	-0.003	4.992	-0.171	-0.171	0.000	0.000	0.000	0.000
36	A	38	TRP	0	-0.025	-0.013	8.279	0.232	0.232	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.038	0.015	11.700	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	40	ASP	-1	-0.942	-0.975	14.663	-0.300	-0.300	0.000	0.000	0.000	0.000
39	A	41	HIS	0	-0.082	-0.054	18.236	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.024	-0.002	20.007	0.011	0.011	0.000	0.000	0.000	0.000
41	A	43	GLU	-1	-0.875	-0.936	21.334	-0.200	-0.200	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.941	-0.969	24.183	-0.175	-0.175	0.000	0.000	0.000	0.000
43	A	45	LEU	0	-0.037	-0.041	24.745	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	46	ASP	-1	-0.922	-0.952	26.396	-0.160	-0.160	0.000	0.000	0.000	0.000
45	A	47	LEU	0	-0.073	-0.027	21.706	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	48	ILE	0	-0.064	-0.015	22.441	-0.023	-0.023	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.881	-0.922	22.153	-0.218	-0.218	0.000	0.000	0.000	0.000
48	A	50	LYS	1	0.893	0.915	24.671	0.148	0.148	0.000	0.000	0.000	0.000
49	A	51	ASP	-1	-0.912	-0.928	22.769	-0.248	-0.248	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.022	-0.004	21.350	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.073	-0.054	18.575	-0.040	-0.040	0.000	0.000	0.000	0.000
52	A	54	ILE	0	0.026	0.005	17.844	0.019	0.019	0.000	0.000	0.000	0.000
53	A	55	ASN	0	-0.065	-0.028	17.902	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	56	ARG	1	0.906	0.943	14.811	0.511	0.511	0.000	0.000	0.000	0.000
55	A	57	ILE	0	0.020	0.019	17.519	-0.018	-0.018	0.000	0.000	0.000	0.000
56	A	58	VAL	0	-0.046	-0.034	11.865	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	59	MET	0	-0.024	0.036	14.457	0.047	0.047	0.000	0.000	0.000	0.000
58	A	60	MET	0	-0.016	-0.013	9.546	-0.137	-0.137	0.000	0.000	0.000	0.000
59	A	61	SER	0	-0.162	-0.168	10.600	0.137	0.137	0.000	0.000	0.000	0.000
60	A	62	THR	0	0.002	-0.019	11.587	0.015	0.015	0.000	0.000	0.000	0.000
61	A	63	GLY	0	-0.030	-0.005	11.934	0.085	0.085	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.030	-0.002	12.537	0.071	0.071	0.000	0.000	0.000	0.000
63	A	65	LYS	1	0.835	0.904	14.013	-0.282	-0.282	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.691	-0.847	18.541	0.057	0.057	0.000	0.000	0.000	0.000
65	A	67	LYS	1	0.897	0.943	22.027	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	68	ASN	0	-0.142	-0.057	23.958	0.006	0.006	0.000	0.000	0.000	0.000
67	A	69	VAL	0	-0.040	-0.026	19.036	-0.003	-0.003	0.000	0.000	0.000	0.000
68	A	70	LYS	1	0.938	0.986	19.059	0.032	0.032	0.000	0.000	0.000	0.000
69	A	71	GLU	-1	-0.757	-0.805	12.374	0.250	0.250	0.000	0.000	0.000	0.000
70	A	72	ILE	0	0.034	0.023	16.359	-0.045	-0.045	0.000	0.000	0.000	0.000
71	A	73	TYR	0	-0.034	-0.033	12.480	-0.006	-0.006	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.824	-0.922	15.048	-0.244	-0.244	0.000	0.000	0.000	0.000
73	A	75	SER	0	-0.003	-0.008	17.378	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	76	ASP	-1	-0.806	-0.898	19.604	-0.077	-0.077	0.000	0.000	0.000	0.000
75	A	77	ILE	0	0.024	0.021	21.945	0.008	0.008	0.000	0.000	0.000	0.000
76	A	78	VAL	0	-0.016	-0.012	22.992	0.005	0.005	0.000	0.000	0.000	0.000
77	A	79	ARG	1	0.916	0.970	26.030	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	80	ASN	0	0.019	-0.004	28.417	0.004	0.004	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.028	-0.033	29.752	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	82	TYR	0	-0.095	-0.041	32.243	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	GLY	0	-0.042	-0.012	33.627	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.830	-0.886	31.994	0.030	0.030	0.000	0.000	0.000	0.000
83	A	85	LEU	0	-0.008	-0.012	30.072	0.004	0.004	0.000	0.000	0.000	0.000
84	A	86	TYR	0	-0.050	-0.034	26.287	0.002	0.002	0.000	0.000	0.000	0.000
85	A	87	VAL	0	0.012	0.003	23.422	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	88	VAL	0	-0.040	-0.009	18.582	0.010	0.010	0.000	0.000	0.000	0.000
87	A	89	GLU	-1	-0.837	-0.901	20.341	-0.096	-0.096	0.000	0.000	0.000	0.000
88	A	90	TRP	0	-0.015	0.004	13.366	0.022	0.022	0.000	0.000	0.000	0.000
89	A	91	LEU	0	0.015	-0.005	17.855	-0.016	-0.016	0.000	0.000	0.000	0.000
90	A	92	ASP	-1	-0.948	-0.972	19.482	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	93	GLY	0	-0.048	-0.035	15.617	0.021	0.021	0.000	0.000	0.000	0.000
92	A	94	SER	0	-0.049	-0.028	15.704	0.057	0.057	0.000	0.000	0.000	0.000
93	A	95	PHE	0	0.014	0.007	12.574	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.030	-0.007	17.844	0.034	0.034	0.000	0.000	0.000	0.000
95	A	97	LEU	0	-0.061	-0.025	21.589	-0.013	-0.013	0.000	0.000	0.000	0.000
96	A	98	THR	0	0.055	-0.003	24.328	0.011	0.011	0.000	0.000	0.000	0.000
97	A	99	GLU	-1	-0.933	-0.991	26.733	0.010	0.010	0.000	0.000	0.000	0.000
98	A	100	PHE	0	-0.001	-0.007	29.266	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	101	TYR	0	-0.007	0.015	32.006	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	102	ASN	0	0.026	-0.008	35.361	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	103	GLY	0	-0.097	-0.022	34.439	0.000	0.000	0.000	0.000	0.000	0.000
102	A	104	GLY	0	0.043	0.016	31.422	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	105	TYR	0	-0.118	-0.046	30.172	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	106	ASP	-1	-0.825	-0.908	25.153	-0.016	-0.016	0.000	0.000	0.000	0.000
105	A	107	HIS	0	-0.055	-0.027	25.885	0.014	0.014	0.000	0.000	0.000	0.000
106	A	108	TYR	0	-0.013	-0.009	21.362	0.001	0.001	0.000	0.000	0.000	0.000
107	A	109	ILE	0	0.007	0.015	18.027	0.004	0.004	0.000	0.000	0.000	0.000
108	A	110	ILE	0	0.013	0.004	20.899	0.023	0.023	0.000	0.000	0.000	0.000
109	A	111	ASP	-1	-0.913	-1.001	18.834	0.277	0.277	0.000	0.000	0.000	0.000
110	A	112	SER	0	-0.026	-0.036	20.925	0.002	0.002	0.000	0.000	0.000	0.000
111	A	113	SER	0	-0.012	-0.009	20.018	-0.006	-0.006	0.000	0.000	0.000	0.000
112	A	114	THR	0	-0.053	-0.040	22.050	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.961	-0.918	24.130	0.123	0.123	0.000	0.000	0.000	0.000
114	A	116	TYR	0	0.008	0.005	23.798	-0.019	-0.019	0.000	0.000	0.000	0.000
115	A	117	GLU	-1	-0.940	-0.974	25.265	0.033	0.033	0.000	0.000	0.000	0.000
116	A	118	VAL	0	0.006	-0.003	20.951	-0.008	-0.008	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.075	-0.048	24.374	0.002	0.002	0.000	0.000	0.000	0.000
118	A	120	GLY	0	-0.011	-0.004	25.157	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	121	ASN	0	-0.051	-0.033	22.410	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	122	ILE	0	0.072	0.028	23.505	0.002	0.002	0.000	0.000	0.000	0.000
121	A	123	TYR	0	-0.028	-0.007	20.792	0.003	0.003	0.000	0.000	0.000	0.000
122	A	124	GLU	-1	-0.915	-0.967	22.959	-0.141	-0.141	0.000	0.000	0.000	0.000
123	A	125	ASN	0	-0.049	-0.011	26.698	0.001	0.001	0.000	0.000	0.000	0.000
124	A	126	PRO	0	0.022	0.014	28.984	0.007	0.007	0.000	0.000	0.000	0.000
125	A	127	GLU	-1	-0.859	-0.924	30.647	-0.059	-0.059	0.000	0.000	0.000	0.000
126	A	128	LEU	0	-0.058	-0.029	28.615	0.006	0.006	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.066	-0.029	28.352	0.004	0.004	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.936	-0.960	32.405	-0.044	-0.044	0.000	0.000	0.000	0.000
129	A	131	ASP	-1	-0.870	-0.939	36.191	-0.019	-0.019	0.000	0.000	0.000	0.000
130	A	132	ASP	-1	-1.018	-1.014	38.338	-0.015	-0.015	0.000	0.000	0.000	0.000
131	A	133	ASN	0	-0.108	-0.065	37.112	0.003	0.003	0.000	0.000	0.000	0.000
132	A	134	HIS	0	-0.001	-0.012	35.503	0.000	0.000	0.000	0.000	0.000	0.000
133	A	135	ALA	0	-0.032	0.002	36.460	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)